


Storm Surge

by WriterJC



Category: Stargate Atlantis
Genre: Drama
Language: English
Status: Completed
Published: 2009-12-02
Updated: 2009-12-01
Packaged: 2017-10-04 02:58:38
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 11
Words: 15,918
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/25187
Author URL: https://archiveofourown.org/users/WriterJC/pseuds/WriterJC
Summary: <blockquote class="userstuff">
      <p>Disclaimer: None of these characters belong to me. No money made, just having a bit of fun with some great characters.</p>
    </blockquote>





	1. Default Chapter

**Author's Note:**

> Disclaimer: None of these characters belong to me. No money made, just having a bit of fun with some great characters.

Disclaimer: None of these characters belong to me. No money made, just having a bit of fun with some great characters.

Author's Note: This is my first Stargate: Atlantis fic ever, so please go easy on me. And of course, wouldn't you know it, I'd pick an AU continuation of "The Storm" . . . . I've only been with these characters for about a month, now, so please forgive any inaccuracies. As for pairings . . . I don't know yet, let's see how it unfolds . . . .

**Storm Surge**

By WriterJC

"Colya!!" John yelled the words into the radio, fear and fury raging through him equal in power to the storm that was bearing down on the city. He had watched Sumner die; another commander would not be lost on his watch. Especially not this commander, not Dr. Weir.

The quiet across the radio link stretched for impossibly long moments as lightning flashed, and the rain started, beating down a punishing assault. Then a booming eruption of thunder sounded, vibrating the very air around him. For one terrifying heartbeat, he'd thought he'd caught the sound of Colya's weapon firing, tearing through the flesh and bone of the woman that he had come to respect as the true leader of Atlantis. But then, he heard something else.

"I want you, unarmed and in front of me in five minutes." It was Colya's voice, the cold tone leaving no margin for error. "If you're not here in the allotted time, I'll kill her and the deal is off."

John closed his eyes, nearly sagging against the railing in relief. Then, pulling himself together, he depressed the button to speak. "I'll be there." Moving in from the cool spray of the rain, he started back toward the inner corridor at a run. Colya was not to be trusted, and he had less than five minutes to come up with a plan.

Elizabeth steeled herself to show no emotion as Colya lowered the gun that had been pointed at her heart. A tiny smirk lit the corner of his mouth as he turned away from her and spoke in a low tone to one of his men. She recognized the gleam she'd caught in his cool gaze; it was the thrill of the hunt. With a flash of insight, she realized that he was enjoying this game of cat of mouse with John. As a military leader, and one who had already bested Genii's own leader, Colya saw Major Sheppard as a worthy opponent. She wondered how she might use this new information to her advantage.

"Dr. McKay," Colya turned back toward the two non-Genii. "You mentioned something about reactivating the shield. Surely you're up to the challenge."

"I couldn't possibly come up with something in the time remaining. Don't you realize what -" Elizabeth could see the signs of oncoming panic in Rodney's eyes. She could also see the lack of patience in Colya's. She didn't want to give the man any excuse to think that the scientist wasn't of any use to him alive.

"Rodney, focus," she spoke calmly, but firmly, looking pointedly at him. "That fourth grounding station can't help us, now. There has to be a way to work around it."

Rodney looked as if he was preparing for round two of arguments as to why there was nothing that could be done when suddenly he paused. "That's it!" And suddenly his expression cleared as he began the rapid-fire speech which spoke of his excitement.

"I don't know why I didn't think of it earlier," he said, then continued thoughtfully, "Must have been the pain and an impending hypoglycemic reaction – speaking of which I'm going to need something soon if this is to continue . . . ."

The Genii soldier who had delivered painful reminders earlier moved forward to grab at Rodney's damaged arm. But the scientist, seeing the intent, drew away, shooting a sharp glare the man's way. "Don't you understand that isn't helpful? Do you _want _to die here?"

At a gesture from Colya, the man backed off.

Rodney turned on Colya. "You understand I need food? It is very difficult for me to work under these conditions. I -"

"You're running out of time, Dr. McKay," Colya interrupted. "If I am satisfied with your performance, we will discuss refreshments."

Rodney was brought up short, clearly not used to being denied food. "Fine," he stated, then with a small sniff he continued with his explanation. "We need to remove the fourth grounding station from the circuit pathways of the rest of the station."

"And how do we accomplish that?" Colya asked.

"I was getting there. The city wasn't built as a single structure, but is composed of several different sections that were then pieced together, something like a gargantuan jigsaw puzzle. The channeling rods that run through the corridors have break-away sections that can be retracted. We'll need to go to each section and manually retract them."

"What'll that do to the city?" Elizabeth asked. "Will the section connected to the fourth grounding rod then be independent?"

"No, not in the true sense of the word. It'll be electrically isolated, though. If my theory is correct, the first bolt of lightning will overwhelm the fourth grounding station and blow it apart, effectively separating it. We reconnect the channeling rods and the original plan is back on track."

"How many channeling rods?" Colya asked.

Rodney turned away and moved toward one of the consoles and brought up a data display. After several moments he looked back toward the group. "Five. All in this section." He gestured toward the portion of the city in question.

"Sounds like a helluva plan." A familiar voice sounded from a corridor leading up from near the gate room. All eyes turned toward John Sheppard who stood, hands held high in surrender, a look of uncaring insolence plastered across his features.

"You're right on schedule, Major," Colya said.

"Wouldn't do to make a bad first impression," John shot back as he was urged in a less than gentle manner up the stairs.

"Dr. McKay," Colya spoke, not looking away from John, "You will direct Dr. Weir in the retraction of the channeling rods. Major Sheppard and I have some business to attend to."

(tbc)


	2. Part 2

**Notes for the Chapter:**

> **Part 2**

**Part 2**

A significant look passed between John and Elizabeth as he watched her walk from the command center with Sora and two other soldiers at her back. He could almost hear the words that she was quietly communicating to him. _Don't get yourself dead. Atlantis needs you. _He could easily have told her the same thing, though he felt marginally better to have her being in Sora's presence than that of Kolya. From the moment he set eyes on the man, he'd pegged him as a heartless SOB with delusions of ruling of the galaxy.

Once the two women were out of view he rolled his gaze in McKay's direction. The physicist was pale and almost visibly shaking. _No fear_, he tried to communicate in a quick glance before focusing on Kolya. Rodney seemed to understand, and pulled himself up taller.

"I'm curious, Major Sheppard. Why did you decide to surrender? It is a clear tactical disadvantage." Kolya's tone was almost conversational.

"It's good to be curious," John replied, having no intention of making this easy on the invader.

Kolya seemed to contemplate that answer, and then casually, he pulled a gun from his jacket and pointed it toward the center of John's head. "I could kill you right now."

John didn't allow himself even the luxury of a blink. Instead he raised his lips in the smile that he'd perfected during some of his more covert assignments. "You could," he agreed, allowing the cold fury to show, if only in his eyes. "But I'm the only person in this city who has the ancient gene necessary to run this place. I'm the only one who can even activate a jumper, and I'm the only one that knows where the C4 is. Oh, and, the tech doesn't work if you're dead."

Kolya re-holstered his weapon, emotionlessly. "You have items to bargain with."

John shrugged, noncommittal. He knew this game.

"Where is the C4?" The tone was quiet, cold.

"Like I said, it's good to be curious."

John caught a slight shift in Kolya's eyes just as he heard Rodney yell his name. He turned into a brilliant burst of pain and light before the room tilted. His last view was of the floor rushing up to meet him.

Dr. Carson Beckett watched as Teyla moved into the passenger section of the puddle jumper and spoke quietly with each of the Athosians on board. He did not understand how she could be so calm under the circumstances. They were literally in the middle of a hurricane the likes of which none of them had ever seen before, and she seemed to be reacting as if this was something she dealt with on a regular basis.

With an inward sigh he turned away, and looked again through the reinforced view screen, consciously attempting to relax tension-tightened muscles. It was no use. The downpour seemed relentless, and worse, he was starting to have doubts about flooding. The puddle jumper wasn't exactly an ark.

"Something is wrong. We need to go back, now!" Lieutenant Ford's voice sounded more loudly than before as he all but pounded a fist against the inactive console.

"Lad, have you not been looking out of this window lately?" Carson asked as he pointed impatiently toward the wide view ahead of them. "If we fly in this we'll die and Major Sheppard will never get any help."

"We've got to do something," Ford insisted. "We're the only back-up he has and it's been too long since we heard anything at all from him! They probably hate him as much as they hate Teyla!"

"I understand that," he said, striving to be patient in the face of the other man's obvious anxiety. "But getting ourselves killed won't help them!" Everyone knew that Ford had developed a sort of hero worship for John Sheppard, which made it even more difficult for him to sit and wait.

They both turned as Teyla appeared between them. Instead of her usual efforts to resolve the disagreement between them she moved closer to the view screen. "Are not the winds lessening?" she asked.

Carson focused more intently on the weather outside, attempting to see beyond the downpour that nearly obscured the view. Apparently the ancients hadn't thought to install windshield wipers when they'd built the puddle jumpers.

Suddenly with that thought, something happened and the window turned completely black.

Carson's mouth dropped open. Before he could get far along the path of worrying about how he'd managed to break the shuttle, a display screen flickered, covering the whole of the window as a real time display appeared. This time though there was no flood of rain, and their vision of what was taking place on the outside was much clearer.

"I did that?" he asked half to himself.

"What'd you do?" Ford asked almost simultaneously, clear amazement in his gaze.

"I don't know. I was just thinking that windshield wipers would have been a nice addition," he confessed.

"Perhaps you should think of what remains of the storm in this area," Teyla suggested, ever focused on the situation at hand.

"Or a way to fly us safely back to Atlantis a little sooner," Ford put in, his intentions equally as clear.

Carson looked between the two of them. Even in light of his apparent success with the viewer, doubts surfaced. Last time he'd played around with the thought component of ancient technology, he'd nearly shot General O'Neill and Major Sheppard out of the sky. He wasn't at all sure he could do this. But they needed him. With a nervous sigh, he settled back into the seat and closed his eyes.

At both their surprised reactions, he looked up and saw that the screen had changed again. This time an animated display appeared showing a route from the current location to Atlantis, including current wind speed and the location of the storm in relation to both the jumper and the city.

"Wow," he breathed, proud of his own effort.

"Looks like you were right," Ford told Teyla. "The winds have died down to about 80 miles per hour. That's definitely better than it was before."

"Still too dangerous," Carson felt obliged to volunteer.

"And it appears that we still have this section of the storm remaining," Teyla pointed to the swirling tail end of the big formation which had its beginning fringes bearing down on Atlantis itself.

"But we have a route displayed for us," Ford pointed toward the flashing green lines. "Why can't we just follow it – like an autopilot? We don't need to be able to see where we're going."

"It won't be an auto pilot," Carson argued, all his previous confidence in the technology fading. "Someone would still have to fly this bird."

"Well it flies through space and automatically docks in the jumper bay when we come back through the gate, how do you know it doesn't have an auto pilot?" Ford challenged, his voice rising again.

"I didn't say it doesn't have one," Carson argued, thoroughly exasperated. "I don't know if it does or it doesn't. I just wouldn't bloody know how to use it!"

Teyla's calm voice broke into their argument. "What is auto pilot?" she asked, her face creased in confusion.

Carson turned toward her. "It's a device that allows an aircraft to fly on its own without the constant attention of the pilot."

"The ship would fly itself?" she pressed.

"Yes," Ford insisted.

"No," Carson disagreed. "That is an oversimplification. A course would have to be set, such as this one," he pointed to the one still display on the screen. "And then the system would have to be turned on. After that someone would have to. . . ."

A slight vibration began beneath their feet, causing Carson to lose his train of thought completely. Utter dread shot through him as he wondered what he'd done this time. Suddenly the route on the screen began to flash and the console lit up.

"Oh crap," Carson whispered as the ship began to rise into the air, buffeted slightly by the force of the winds.

\--

A/N: I hope you all are still enjoying this. Thanks to everyone for the wonderful reviews and the lovely welcome to the fandom.


	3. Part 3

**Notes for the Chapter:**

> **Part Three**

**Part Three**

Elizabeth moved along Atlantis's corridors, her silence matching that of her escorts. Though Sora remained watchful and cautious, as did the other two soldiers, Elizabeth thought there was something more in the Genii woman's demeanor.

Sora cut her eyes toward Elizabeth, catching her observation. Her expression hardened and coldness glittered from her eyes, but instead of being reminded of the woman's useless vendetta against Teyla, she became thoughtful, an idea percolating in the back of her mind.

"How much farther?" Sora questioned, the words echoing over the sounds of four booted pairs of feet.

"Not very much," Elizabeth replied, seeing ahead the area where the wide corridors narrowed slightly and were less ornately decorated. Many of the scientists hypothesized that these areas were mostly used for maintenance functions and were thus less adorned. But Elizabeth thought that every section of Atlantis that her eyes had touched was beautiful. It would be an injustice on a mammoth scale if it should fall into the hands of people who only wanted it for the purposes of war.

She came to a stop outside of a door with a small irregular symbol on its outer surface. It slid open when she touched the panel on the wall alongside it which bore a matching symbol.

Dim lighting, illuminated at half-level, revealed a narrow area beyond. It hardly seemed fair to call it a room as its width was little more than three feet across. It extended several yards to a darkened control panel at its opposite end. On a side wall near the panel at roughly chest height was a round metallic object which vaguely reminded her of a steering wheel.

"It's pretty tight in here," she told Sora, stepping slightly to the side to allow her to see the close quarters.

Sora peered past her then turned toward the guards. "Remain here," she ordered brusquely. The guards obeyed without question, stationing themselves just outside of the open doorway.

At the far end of the wall, Weir came to a stop, taking in the console. She reached automatically for the communication device at her ear before remembering that Kolya had taken it.

Resigned, she took the walkie-talkie Sora extended in her direction. "We're here," she announced after depressing the talk button.

Silence greeted the statement for several moments before Rodney's voice sounded across the connection. Weir noticed the more highly pitched tone of his voice and immediately feared the worst.

"Yes the panel is lit," she answered his original question quickly, and then pressed on to the more urgent worry. "How are things going there?"

"Oh, you know, big –." Rodney's voice ended abruptly and was replaced by Kolya's.

"Focus your attention on the task at hand, Doctor. Both of you." The last of the menacing words were obviously intended for Rodney.

"Hurting us doesn't help your people's cause," she said, hoping still to reason with the man.

"I determine what helps my people's cause," he replied, unmoved. "What does not help will be eliminated. Continue your work."

After a moment, Rodney returned to the link. "Dr. Weir?"

She tried not to sound defeated. "I'm here, Rodney. What do I need to do?" She listened as he explained the simple procedure that needed to be accomplished at each of the stations. When she was sure she understood, she handed the walkie-talkie back to Sora.

"Kolya can't be trusted," she told the other woman quietly as she punched in the few keystrokes on the console, and then moved toward the wheel and began to turn it counterclockwise as Rodney had outlined.

"You do not understand my people," Sora sneered.

"What if he decides you aren't good for the cause?" She pushed just a little more, testing the other woman. "What if he decides that he's better qualified to lead your people, and that Atlantis should be his only? What then? Will you follow him, or will you be eliminated?"

Sora's eyes widened and Elizabeth wondered if the Genii woman hadn't already asked herself those same questions.

"You will not talk!" Sora's voice rose bitterly, and she hardened her stance and pointed the weapon more directly at her.

Elizabeth stiffened, and worried that she had gone a little too far, but then the weapon was gestured back along the narrow area.

"You are done here and we will go to the next position."

Elizabeth nodded and stepped around the muzzle of the gun and led the way out. She caught the gazes of both guards as they stared intently at the two women.

"Relax, Doc, we're almost there." Ford's almost cheery voice rang through the cabin of the bucking puddle jumper.

"How can I relax?" Carson demanded. "We're in the middle of a bloody hurricane!" His eyes hadn't moved from the display during the entirety of the journey from the mainland. He was half afraid to think, least he cause some chronic system failure. And worse of all, the theme song from Gillian's Island kept playing through his mind taunting him to the follow the thought to its conclusion – the lot of them lost for all time in some freak storm created by some random technological failure as a result of his misuse of the ancient gene.

"Yeah, but only for about five more minutes," Ford replied. "Then we can get in and help the Major."

"And how are we supposed to do that?" Carson demanded. "We have villagers and children on board."

Ford grinned at him as a side panel opened and the portable life-signs reader appeared near the pilot's seat. Carson grabbed the device and gave it to the lieutenant with a dirty look. All this ancient mind-operated technology made him feel out of control and in over his head. "And now, what's the rest of the plan?" he demanded.

Ford looked him over in a measuring way. "You stay with the villagers and the jumper. Teyla and I will go give the Major some back-up."

He looked between Teyla and Ford. They were both warriors in the true sense of the word. But he, Carson Beckett, was a doctor. He didn't walk around with a gun and shoot the bad guys. It wasn't his thing and he wasn't good at it. He also wasn't good at letting his friends go out and fight alone when he might do something to help.

He grimaced and sighed internally. "No, I'll go with you."

"Good man." Ford seemed pleased.

"Are you certain?" Teyla asked, her gaze pressing into his.

"Of course, I'm sure," he responded, hoping she wouldn't call him on it. "All of us have had some training in the use of the weapons and self-defense measures. Besides, if it comes down to it, I've got a healthy supply of hypodermics and I'm not afraid to use them."

John woke with a start, gasping and sputtering. A smell, bitter and heavy seemed to sear a path through his nostrils and into his skull. He coughed, trying to clear away the noxious fumes, but it only added to the sudden pounding ache in his brain. Instinctively he tried to move away, to see what it was that was causing the problem, but his body wouldn't respond to his commands and it took several moments before the hazy world resolved into something recognizable.

Coughing a few more times, he allowed his eyes to focus on Kolya. The man was seated across from him, closing the lid on a small metallic canister.

_Great_, John thought, as the container disappeared into one of other man's pockets, _Probably the Genii equivalent of smelling salts. Only worse. _As the scent made its way out of his nasal passages, other things registered, like a near loss of feeling in both arms. He looked downward, and found that both his forearms were strapped tightly to the chair's armrests. Flexing his fists, he tested the bonds before checking to see what means had been used to secure his legs and feet.

"Sorry I fell asleep there," he said, glancing back up at Kolya. "Don't think it means that you're boring or anything." He looked beyond the Genii soldier as a brilliant flash of lightning illuminated the darkened skies outside. The rain was sheeting against the windows as the storm bore down on them near full force.

Kolya ignored the remark, and leaned forward slightly. "Where is the C4, Major?" he asked in a low-toned voice.

John craned his neck, hoping to see the rest of the Command Center which was situated behind him. A couple guards were still there, as was McKay, punching something frantically into a handheld device. Sheppard knew that look. The good doctor's plan was working and he was heavily engrossed in some calculation or another. Weir was nowhere to be seen.

He turned back to Kolya. "Storm is getting pretty rough out there."

One of the guards approached rapidly and buffed him alongside the head. It wasn't an especially hard hit, a love tap, really, but the quick tilt of the room and the sharp spear of pain reminded him vividly that he'd recently been hit in that same spot.

"That is not an acceptable answer," Kolya explained.

"I sorta got that," John responded, wishing he could wipe away the itchy feeling that began as blood trickled along the side of his head. The dry patchy sensation near his temple told him that this wasn't the first blood he'd bled that day.

"Where is the C4?" Kolya asked.

John glared at him. "I forget. Head injury, you know."

The soldier who'd whacked him in the head stepped to his side. There was a deep grinding sound as the man pulled what looked remarkably like an M-9 bayonet knife from its holder. A noise echoed from the opposite side of the Command Center and Sheppard had a sneaking suspicion that McKay had just dropped whatever handheld device he'd been holding.

"Dr. McKay." Kolya looked beyond John to speak to the gifted scientist. "Please explain the status of your plan to Major Sheppard."

John had to turn his neck into a painful position to see his comrade. The look of complete absorption in his work was gone, replaced by dread and uncertainty. He obviously didn't want to be a participant in whatever Kolya had up his sleeves.

"Th-the re-grounding process is nearly complete," he explained, looking uncomfortably about the room. "A lightning strike took out the fourth grounding station as I suspected. I have to keep refiguring the equations, but it appears that the plan is working."

"You may go back to your work, Doctor McKay," Kolya told him.

Sheppard was buoyed by the sarcastic retort that he knew McKay had bitten back. It brought the hint of a smile to his features as he turned back to face the Genii.

"Dr. McKay is quite an asset," Kolya stated.

"Yes, we tell ourselves everyday how lucky we are to have him," John replied, trying to ignore the knife moving in closer, taunting.

Kolya reached for the walkie-talkie and spoke into it, asking Sora if she could complete the reconnection of the final channeling station. Sora's affirmative answer started a warning bell in the back of John's mind.

"Have the guards return Dr. Weir to the Command area while you finish the task," Kolya ordered. After ending the communication, he looked at John. "Where is the C4?"

"Go to hell."

The hand with the knife moved.

\---

A/N: Sorry about the long delay. I hope you're all still enjoying this. Organized Chaos - no wetness this chapter, but there is wetness to come eventually! John has a few other issues to worth through for the immediate future . . .


	4. Part 4

**Notes for the Chapter:**

> **Part Four**

**Part Four**

Rodney jerked reflexively at the muted grunt that escaped Sheppard when Kolya's goon jabbed him in the arm. All thought flew out of his head and he nearly dropped the handheld computer again as he recalled vividly his own run-in with the same knife.

"Where is the C4, Major?" The question that Kolya had been asking over and over reached his ears. The Genii leader was calm and unaffected by the suffering he so casually caused.

"Where you'll never find it," Sheppard replied, his voice strained.

Kolya's man moved in again, and Rodney cried out. "Can't you see he's not going to tell you anything? If you're going to take over Atlantis, you'll find it eventually, anyway!"

"Why would I expend such effort, Doctor McKay, when the solution to the problem sits before me?"

"B-Because . . . ." Rodney cast around for an answer. "Because he can help you in other ways. . . ."

"Rodney –." Sheppard interrupted, his tone suggesting that he didn't need to be defended, but Rodney kept talking. He wouldn't stand by and watch another being tortured.

"He's the one carrying the ATA gene," he blurted the same argument that Sheppard had used earlier. For all of the times he'd envied the Major's affinity with using the Ancient technology, it felt odd to be using it as a bargaining point – ignoring the little white lie, of course. "And he uses it like he was born to it, almost instinctively. He's the best chance you've got of getting this city to work for you."

"Better than you?" Kolya asked, focusing cold eyes intently on him.

Rodney faltered mentally, and fought the urge to take a step backward. The his natural inclination kicked in. "Of course not," he responded. "What I'm trying to explain to you is that through some freak of nature, he's the key to everything."

"I'm flattered . . . I think." He heard John mutter.

"All the more reason to break him, now," Kolya said, and refocused on John, clearly demonstrating that the conversation was of no more interest to him.

"He isn't some animal to be broken," Rodney argued, panic at the possible return of the knife bearing down on him. "He's a human being who deserves to be treated with respect and dignity."

Kolya's gaze didn't waver from John. "His worth is yet to be seen."

"Is this not unusual?" Teyla's curious voice sounded.

Carson looked to where Teyla was looking, and his heart dropped into his stomach. For a moment her could only stare in the hope that he was hallucinating. Just when he'd been getting used to the autopilot thing, everything was going to pot. This was why he didn't trust himself with this sort of technology. He didn't like it and it clearly didn't like him.

"That is weird." Ford spoke from the opposite side of the console, the nervous quaver in his voice not entirely camouflaged. He tapped a few keys on the console, none of which responded. "What did you do, Doctor?"

Carson's breath was beginning to come in quick gasps and he hoped that he wasn't headed for full fledged panic. "I didn't do anything!" he forced the words out. "The jumper was doing all of the work, remember?"

"So explain why we're about to crash into the ocean!" Ford demanded.

"Arguing will not help the matter," Teyla reminded them. "Is there not something more we can do? Can we not fly the ship, Doctor?"

"What?!" Carson demanded, incredulous. "I've no idea how to make it stop. He'll, I'm not even clear on how I started it. We're going into the water in the next thirty seconds and there's nothing I can do about it!"

"Everyone, brace for impact!" Ford yelled back into the passenger section.

As the waters came ever closer, the thoughts of Gilligan's Island returned with guilty force as the roiling waters rushed up to meet them.

Elizabeth set the pace with the guards at her back, as she made her way back to the Command Center. She had no idea as to why Kolya wanted her back before even allowing her to complete the final channeling rod reconnection. It was worrying, and as little as she wanted to bow to his demands, she also needed to know what was going on.

She faltered half up the stairs when her eyes settled on the tableau there, then continued along more slowly, needing to confirm the situation. John was tied to a chair that more or less faced the steps. Kolya sat across from him, his back to her, while one of his men stood alongside John with a huge knife in his hand. There was blood on the knife. Her mind stuttered over that realization for several moments before her gaze drifted toward the growing area of darkened wetness on John's arm that had nothing to do with his having been out in the rain. There was another area, she realized to her horror, on his leg. Her eyes slowly rose to meet John's.

The usual cocky grin was not in evidence. He was pale and perspiration beaded on his brow. He didn't seem happy to see her. As the soldier with the knife started toward her, she began to understand why. Her heart plummeted to her toes.

"No!" Rodney's outburst from a far console drew her gaze. He was quickly subdued by another of the guards.

The other two guards were still at her back. Kolya remained seated, never turning to face her, and the one with the knife was before her. There was nowhere to run to, as if she would. She looked back toward Major Sheppard and steeled herself for what was to come. Both he and McKay had already suffered at the hands of this merciless Genii soldier; it was her turn, now, it seemed.

The soldier grabbed her arm. Refusing to be dragged, she walked alongside him until she was standing in Kolya's line of sight. Still, the Genii leader didn't look in her direction, not even when the soldier pressed the point of the knife into the skin at the back of her throat.

"Where is the C4, Major Sheppard?" Kolya asked tonelessly.

Elizabeth could see the struggle on John's face, but she knew ultimately what his response would be.

"I have to show you," he said, "It's not a place I can explain."

For the first time during their acquaintance, she thought she saw Kolya smile.


	5. Part 5

**Notes for the Chapter:**

> **Part Five**

**Part Five**

Beckett squeezed his eyes shut and gripped the armrests for dear life as the waters closed in over the puddle jumper. A litany of impolite words played through his mind and he vaguely noted the way the shuttle seemed to rebound after its initial entry. The beating that the shuttle was taking from the winds was immediately gone, leaving them surrounding by a cocoon of near stillness that was almost as unnerving as the storm had been.

Carson open his eyes a notch experimentally, immediately thereafter his jaw dropped.

All thoughts of death were forgotten as he gaped at the previously darkened view screen. The clear surface had changed. Transparent once again, it allowed them to look out upon the simple beauty of the ocean beneath the city. All of Atlantis clearly wasn't above the surface.

Carson imagined that if not for the darkened skies and the storm raging overhead, the sunlight shining through the water might have reflected like brilliant gems through the intricate designs that extended from the edges of the city. The segments were reminiscent of the stained glass windows that the Ancients appeared to favor.

A thrill of excitement washed through him at the thought that he was one of the first to see this section of the ancient abode in tens of thousands of years. The rest of the scientific teams were going to be beside themselves when they learned that the puddle jumpers were viable under ocean vehicles as well.

"Wow." Ford's surprised murmur drew him out of his awed observations. He spared the younger man a glance.

"Yeah. Wow's the word for it." He was transfixed by all that there was to see. The jumper steered itself smoothly amid the many vari-shaped surfaces and odd protrusions. Lights were coming on, shining down into the waters illuminating their way as they went. It was as if the underside of the city was welcoming them just as inner portion had when they'd arrived from Earth.

"Might that be the area to which we are going?" Teyla asked the practical question and pointed toward a large rectangle of dim light ahead.

Carson shared a look with Ford.

"Sounds good to me," Ford volunteered.

"We'll soon find out," Carson commented as the jumper began to slow. It came to a stop in what seemed to be the center of the light. And then the jumper began to rise through the waters upward into an opening beneath the city.

There was a small thump as they settled against something and then continued to rise. The waters drained away quickly and the door release at the back of the shuttle hissed as it opened.

"Looks like we're here," Aiden said.

"Wherever here is," Carson added.

"So we stick to the plan," Ford said, picking up his gun and standing.

"We stick to the plan," Carson agreed, following Ford and Teyla's lead.

\--

"Stop." Kolya quietly called a halt as he took the walkie-talkie from one of his men.

John limped the extra paces which carried him to the wall and leaned against it. He completely ignored the guard who had moved beside him, and tried to ignore Dr. Weir's eyes on him. He knew the look he'd see there, it was the one that silently asked if he was okay.

Of course he wasn't okay; he had two holes in his body that didn't belong there. Kolya's man had known what he was doing, too. The wounds were deep enough to slow him down, but not enough to put him completely out of the action. But that didn't mean that they didn't both hurt like hell.

Bending slowly, he checked on the pieces of cloth that had been tied around the leg wound. He didn't even want to think about the medical procedures Beckett would have to perform on it when they got out of this. Not if, but when. As far as he was concerned things were proceeding exactly according to plan. Well, sorta exactly according to plan. What he'd had in mind hadn't included two stab wounds, being tied to a chair, or having Elizabeth along for the ride. In the grand scheme, plans had gone far worse. It was always the details that sent the plan into the toilet.

Moving back into an upright position, he looked across at Weir, trying to get a subtle message to her. She stared steadily back. He hoped that meant that she understood that she needed to be ready when he made his move.

Sora's disembodied voice sounded across the radio link. She said something about needing more troops for reconnaissance in the section of the city where the channeling rods were located and named the men she wanted. Kolya agreed, and then clicked off the connection.

"What more lies in that section of the city?" The Genii commander asked.

"We haven't explored all of those areas yet," Weir answered him coolly. "We believe them to be predominately maintenance sections."

"Could be monsters," John piped up. "Or rats. Great big ones."

Kolya ignored the comment, and ordered one of the guards to go to the area and to report back what he saw. He added something more that was too low for John to hear, but it still piqued his curiosity. Was all not peace, love and harmony in the Genii camp or was Kolya just being cautious?

John didn't really care. He was just glad that he had one less guard to deal with.

"Continue," Kolya ordered as the guard started back in the opposite direction.

John gathered his strength before he pushed himself away from the wall and continued to move painfully down the corridor with Kolya's remaining flunky shadowing him. The Genii commander moved along behind them, keeping Weir close by his side.

\--

"What the . . . ?" Rodney tapped rapidly on the computer keyboard, going through his calculations once more. Something just wasn't right. And it had been before. He would not accept the idea that he'd miscalculated.

One of the guards that Kolya had left behind moved in closer. He wasn't the madman with the knife, but he was equally annoying. With a suspicious look, the soldier looked over all of the active screens.

"Do you mind?" Rodney asked, shooting the man a disgusted look. "Trying to save the city remember?"

The guard stared at him a long moment before returning to his previous position a few steps away. But he continued to watch closely as if in warning.

Rodney rolled his eyes. As if one of Kolya's lackeys could possibly have any clue what he was looking at. Or understand the magnitude of the project that was being undertaken. Atlantis wasn't just some military outpost to be fought over. It was a living scientific marvel. It needed to be preserved at all costs.

The final channeling rod had been put back into place, and if with the lightning and the winds and the debris that would follow, the city would be completely vulnerable.

If lightning was to strike now, he wasn't exactly sure what was going to happen. And Atlantis was far too big a target to go unscathed for long in a storm of this magnitude. The survival of the city was on his shoulders. Everyone, even the bad guys, was depending on him.

Panic teased at the edges of the adrenaline that kept him going. Always before his teammates were there to keep him on task. But now he was alone. No one else to --

What was that? What was that odd reading? Refocusing, he typed several commands into the keyboard and tracked the power drain, displaying it on a smaller monitor. He surprised a start of excitement. The drain was emanating from a portion of the city that had sacrificed itself centuries earlier when the shield had begun to fail. Could this mean?

A brilliant flash of lightning shown through the large window overhead, reminding him that there was little time. Determined, he took a final reading and went back to his calculations, this time allowing for the changed energy consumption. Perfect.

He transferred the new algorithm to the program he and Zelenka had created and executed it. Now they were ready.

\--

Elizabeth knew that John was tiring. He was favoring his right leg more, and his steps were slowing noticeably. Making matters worse, the corridor they were taking was on a slight incline, no doubt increasing the strain on his injured leg. He had earlier taken to walking with a hand along the wall, but Kolya had insisted that he remain the center of the walkway.

He glanced back over his shoulder. The dim lighting seemed to accentuate his pallor which, alongside dried blood mixed with perspiration, only added to an increasingly grizzly appearance. But it was the shadowed eyes, utterly devoid of humor, that resonated with her.

"We should let him rest," she spoke up, turning on Kolya. "Nothing is gained by driving Major Sheppard to exhaustion. The C4 isn't going anywhere."

Kolya completely ignored her request, continuing along the corridor. It was as if she hadn't spoken at all.

"What did you expect, Doctor?" John asked, his words ever so slightly slurred, his voice not nearly as strong as it had been when they'd left the command center. "Mercy for one's enemies is what our Genii neighbors might call a tactical disadvantage."

"That's a very shortsighted viewpoint," Elizabeth couldn't resist saying. "We have a mutual enemy. If we work together we can defeat him. Together we are stronger, we could form an alliance with other words and form a formidable force. There is a saying on our world 'United we stand.' That is the way we can stand against the Wraith."

"We also have a saying, Doctor," Kolya replied, though he didn't look at her. "An army of many is only as strong as its weakest link. Without Atlantis, you have nothing to offer."

Elizabeth thought she caught a half snort from John, and then, "I think he just called us the weakest link." He stumbled slightly, but continued on, listing again toward the wall, uneven steps placing him on a crooked path toward it. "Probably better than being called the missing link. Why don't you tell him some of the great examples of how people on our world worked together for the betterment of mankind?"

Elizabeth's eyes were locked worriedly on his back, and for several moments she struggled over the question. Then, to Kolya, "Eventually your people are going to have to change their way of thinking. A world cannot survive . . . ."

Suddenly, she caught a view of John from her peripheral vision. One minute he was limping along, the next, he went down heavily. "John!" She called his name, and instinctively tried to move toward him.

* * *

A/N: Again forgive the delay. Major computer problems. And now, I totally have to hurry and finish this. Spoilers are flying around about "The Eye", nevermind copies of the episode, and I'm not allowing myself near any of it until I finish this. Talk about feeling an urgent need to get something done!

Also, since fanfiction-dot-net has been eating my scene dividers, I've gone to some different characters. Hope they work!


	6. Part 6

**Notes for the Chapter:**

> **Part Six**

**Part Six**

The floor had come up a lot quicker than John expected, and pain resonated throughout his body. Despite the adrenaline that coursed through his system, every reaction felt sluggish and weighted down. He heard Elizabeth cry out and approaching footsteps as he grabbed for the contraband that he'd stashed behind an ornate section of the wall.

He rolled, pulling the pin as he went, and then tossed the smoke bomb beyond Elizabeth, into the space between Kolya and his man. Thick smoke began to pour out of the narrow canister. He inwardly cheered as Weir continued running until she was on his opposite side, allowing him to use the small advantage the smoke bomb afforded to gather several more items from their storage spot.

He twisted back toward the two Genii, and aiming through the growing smoke cover, squeezed off one shot with his .9mm. A surprised gasp of pain registered distantly as moved on to the next target. Before he could pull the trigger, an iron fist slammed into his chest. John only vaguely registered the jarring motion of being slammed backward onto the floor.

\-- --

The life signs reader registered four persons somewhere up ahead. Aiden knew that all of those dots could not represent friends as Major Sheppard had clearly communicated that only he and Doctors McKay and Weir remained alive in the city. That was only three friendlies.

He glanced back toward Teyla and Beckett. Teyla was a solid warrior, Beckett looked a little nervous. Still, three against four really wasn't bad odds, especially with the element of surprise and superior fire power on their side.

"We need to get in closer," he whispered to his two friends, "find out who they are."

"How do you propose we do that?" Beckett asked. "I'd be surprised if they don't know we're already here what with all the noise that was made when we landed in that underwater bay thing."

Ford couldn't argue Beckett's assessment, but they had to move forward with what they had. They had gotten out of what he had already dubbed the lower jumper bay as quickly as they could and were winding their way through the lower levels of the city.

"It appears that they are moving toward us," Teyla pointed out. "Why do we not lie in wait until they approach?"

Aiden rolled the idea around in his head and decided he liked it. "Okay. But let's split up a bit." He pointed toward the device. "They're going to have to come up this cross-corridor. We can hide on either side here."

Both Teyla and Beckett nodded in agreement and they made their way quietly to the designated areas. Teyla and the doctor occupied one side of the hall, while he took up the other side. He kept the life signs indicator with him.

As the four dots drew ever closer, he nodded across the small expanse to his companions, notifying them that it was nearly time. Teyla nodded in understanding. Beckett swallowed hard and gripped his weapon more tightly. Aiden looked into the doctor's eyes, willing him the strength to get through this. He then flattened himself against the wall, preparing to wait out the few seconds before the group of four would appear.

He was preparing to signal Teyla and Beckett when he noticed that something was changing around them. The other two seemed to recognize it as well. All eyes were drawn upward in confusion as it dawned that the lights were getting noticeably brighter.

\-- --

The world was hazy and insubstantial. But he felt an urgency that prodded him to fight against the desire to just quietly let himself be taken under. The sounds which floated about above him began coalescing into recognizable words.

". . . .can not do it, Doctor. You are not a warrior." Kolya's voice. As cold and nasty as ever.

"I'll do what I have to to save my people." That was Weir. That must mean. . . .

John's eyes shot wide. He blinked several times to be sure that the sight that greeted him through the rapidly clearing smoke cloud wasn't an illusion. Dr. Elizabeth Weir was standing, in a perfect policeman's stance, with _his_ .9mm pointed toward Kolya.

The Genii had one foot under him as if he'd been on his way back to his feet. Blood was splattered along the side of his face, which confused John until he noticed that Kolya's weapon was a couple yards away and that there was a bloody looking tear near the shoulder of his uniform. That was when he remembered the shot he'd fired just before he'd gone down.

He'd been shot!

He struggled into a half-sitting position with a grunt. His chest, and every other part of his body, protested mightily making their complaints known. With all the dizziness, pain and nausea flying around, never mind the complete lack of a big bloody hole in his chest, no way was he dead.

A stiffening in Elizabeth's body revealed her awareness that he was back among the land of the living. "You okay?" she asked over her shoulder, never looking away from Kolya.

"I'm not dead," he managed, deciding that he'd take the pain if it meant that he was still alive. Then confusion settled in. "Why am I not dead?"

"Probably the materials in your flak jacket," she replied. "Our bullets are stronger than their bullets."

"Oh. Good." The nausea and dizziness was starting to abate, and John figured it was time that he crawled back into the fray. He got his uninjured leg beneath him, braced his uninjured arm against the wall and levered himself into a semi standing position. He gave things a moment to steady themselves before straightening completely and starting to walk.

"And you thought we had nothing to offer," he chided Kolya as he checked that the downed Genii soldier would not be causing them any more trouble. He took his gun for good measure. The weapon didn't even rate compared to his P90, but Elizabeth was looking pretty comfortable with the 9 mil, and he had no intention of dividing her attention away from Kolya to retrieve it.

He turned back to face Kolya. "So, how about we give you a tour of what we like to affectionately call the brig?"

"You should kill me." Kolya told him, not moving.

"Thanks for the advice," John snapped. "But that's not the way we do things around here."

"I will be your enemy forever, and I will always come back."

"Aw, threats. How touching." John gestured with the muzzle of the Genii weapon. "Get up. Slowly."

He held his finger on the trigger and his eyes locked on the other man as Kolya began to rise. He knew given even half a chance, the other man would try something. He almost hoped he did; it would give him a reason to make sure that he never had a chance to fulfill his words.

As he contemplated exactly what they would do once they'd completely taken Atlantis back, the overhead light inexplicably began to brighten. He wasn't sure what it meant, but he had just enough time to register the really bad feeling he had about it before the corridor was suddenly plunged into complete darkness.

He knew in the milli-second before the breath was knocked out of him that Kolya had made his move.

\--

A/N: I have been having great fun writing and posting this story. You guys are wonderfully encouraging! Oh, yeah. . . .awfully sorry about yet another evil cliff. . . . And the whumping continues. . . .


	7. Part 7

**Notes for the Chapter:**

> **Part Seven**

**Part Seven**

"Oh crap."

Rodney's words sounded amid the eerie glow of the battery operated lap tops. For one heart-stopping moment, his mind froze as he contemplated the idea that he might have broken Atlantis.

Just moments before, the plan had been working perfectly. He'd completed his calculations and the mother of all lightning strikes had hit the city, jumping from one place to the other and sparking other smaller bolts. The energy had kept building until it topped out the scale. The lights had started to get bright right after that and then nothing.

A breath passed in the darkness before he heard the shuffling feet of the nearby soldiers. Their nervousness was making him nervous.

"Nothing to worry about," he said in direct contradiction to his previous comment. Hopefully 'Oh crap' didn't translate well. Last thing he needed was for over anxious soldiers to start shooting up things in the dark.

Then suddenly, there was a spike on the lap top and with a sound like a generator winding up the lights came back on. He watched the screen as many other systems began to cycle back in as well.

"What happened?" the nearest guard asked, looking uncertain as to how to respond to the situation. McKay was sure that black outs in ancient cities wasn't covered in Genii Generic Bad Guy Training 101.

Despite all of his scientific knowledge and the many things he'd experienced in his career, he was still a little confused, too. Then suddenly, things began to click in his mind. An uncontainable grin spread its way over his features. It was simplicity itself.

"Circuit breakers. It's circuit breakers!" He began to pace as worked his way through the idea. "The Ancients must have installed a fail safe to protect the city from a power overload," he said, completely excited by how flawlessly the system had worked even with the presence of the power generators that had been brought from Earth. "It obviously kicked in when the lightning strikes became overwhelming and just shut everything down. No doubt, when the levels decreased they reset everything. Although, considering the incredible amount of power the system was able to handle prior to the fail safe . . . ."

He paused at the blank look that came over the guard's face. "Ugh, never mind. Part of the plan." He waved the man away and returned to his computer screen. That had been a pointless conversation. He had much more important things to do, like making sure that they'd be able to hold on to any power they may have been able to harness, and after that, masterminding a way to get away from these three goons stationed in the command area so that he could check on his friends.

\--

John barely had time to react when what felt like Kolya's shoulder collided with his midsection. Instinctively, he drove his arms downward, slamming the butt of the Genii weapon against flesh and bone. Despite the grunt that Kolya emitted, his momentum sent them both hurtling toward the unyielding material that made up Atlantis' walls. John's back took the brunt of the impact.

Pain receptors gone into overload took John's legs out from under him and he dropped like a stone taking Kolya with him to the floor. He heard the gun clatter away somewhere beyond his head. Having landed more or less on top, John tried to press his slight advantage by working to pin the broader man. But his reflexes were slow and being concussed, stabbed, stabbed again, shot, and then slammed into a really hard wall had a way of taking the strength out of a guy.

Still, he wasn't doing too awfully bad and wasmanaging to keep Kolya relatively under control until the man's fist made contact with the side of his face. He tumbled to the side off of the Genii, landing on the wounded arm.

Instead of going for the gun as John had expected him to, Kolya followed him over and continued the punch fest. That was when it occurred to John that this was so much more than war; it was personal, between himself and Kolya. Atlantis barely fit into the picture. Kolya would not accept being bested by another man and wanted to prove with his bare hands that he was warrior chief. John had no problem with that; he had more than a little aggression to work off against the other man.

Suddenly the lights came back up, and Elizabeth was there, still holding the .9 mm. She directed it toward their new position and ordered Kolya to freeze. The Genii was leaning over him, had one hand clutched in the material of John's vest, while one arm was drawn back, preparing to throw yet another punch.

John stared up at him, having a nearly irresistible urge to get in one more blow, to put the other man's lights out. But that'd only mean that they'd have to carry him, which wasn't a good bet at the moment. So, he satisfied himself with taking in the beginnings of the ugly bruises the Genii would soon be sporting.

"Lets try this again, shall we?" he gasped, after extricating himself from their positon on the floor. He willedhimself to make it back to his feet without stumbling. He then retrieved both Genii weapons, and after tucking one into the back of his pants, he pointed the other at Kolya.

The Genii's cold eyes held the promise that there would be another time, but he didn't speak, and John didn't have to ask him to get up and start walking.

\--

By the time Ford realized that the light from the life signs reader was shining like a beacon in the night, he caught the muted sound of a footstep. The noise was almost right on top of him. Before he could react, the lights came on, bringing him face to face with the blonde woman from the Genii home world and three other soldiers. The three men all had weapons trained on him.

He brought his hands slowly upward in surrender, locking gazes with Sora. Her expression was brutal.

"Where is Teyla Emmagan?"

"Here I am." Teyla announced, gathering the attention of the Genii. They turned as a unit to see Dr Beckett and Teyla with P90s leveled on them. Ford brought his weapon to bear, covering them from the other side, effectively trapping the Genii between the three of them.

"Drop your weapons," Ford ordered, clearly the one in charge.

The three guards looked to Sora for direction. After throwing hateful looks all around, she nodded and the men slowly lowered their weapons to the floor.

"Radios, too," Aiden added, pointing toward the devices. That drew another furious glare from Sora, but they complied and the electronics were dropped to the floor alongside the guns.

"Dr. Beckett," Ford called. "If you would retrieve their weapons?"

"Happy to lad." The doctor replied, stepping somewhat nervously away from Teyla toward the pile of weapons.

One of the soldiers shifted as Beckett drew closer and Ford got the point across with a gesture of his P90 that there was a bullet with the soldier's name on it if he tried anything. The soldier settled down with a glance toward Sora.

He caught Beckett's nod of appreciation as he moved out into the cross corridor. It only took several moments for him to gather all of them up into his arms. Peripherally, Ford noted that as the doctor started to straighten back up, his body jerked in shock as he stared beyond the Genii. The weapons began to spill from Beckett's arms just as a shot rang out. And then all hell broke loose.

\------

A/N: Wanted to get this one up before fanfictiondotnet goes down on Sunday. You guys have been marvelously encouraging. Thank you so much!

B7-kerravon, I'm honored that you like it better than "The Eye". I've got my very own downloaded copy and it's killing me not to watch it. I will admit that I've watched "The Defiant", though. . . .:-)

ErabuHikari – w/ regard to writing for the show: I wish!!

Hope you are all still enjoying this!


	8. Part 8

**Notes for the Chapter:**

> **Part Eight**

**Part Eight**

Carson had long heard the saying that one's life flashed before one's eyes just before they died. Though he'd always discounted it as a medical improbability, he was ready to revise that opinion when he saw the Genii soldier appear at the end of the long corridor wielding a big triple barreled gun.

All of the events that led to his arrival at Atlantis rushed to mind, making him wonder that such a fantastic journey would end there and then at the apex of a dimly lit corridor.

He didn't remember dropping the arm load of weapons, or even ducking for cover. But the flashes of light burned their way onto his corneas, and the sound rang through his ears.

He thought he heard Ford yell something and then it seemed that bodies were moving everywhere. Four of those bodies wore Genii uniforms and they were moving toward the weapons. It was reflex that caused him to kick the guns, scattering them before Sora or either of the men could reach them.

Another shot sounded and one of the Genii jerked before crashing to the floor. The other three, it seemed, froze in place. Carson's gaze darted between the downed man and the corridor ahead. He blinked. It was completely empty.

"Get up!" Ford's orders toward the remaining Genii penetrated, jumpstarting him to action. Moving on automatic, he went to the downed man's side and quickly began to check him over. Even before he tried for vitals, he knew it was too late. A life lost.

"What the hell happened?" Aiden demanded as he and Teyla secured Sora and the other two guards with restraints.

Carson rubbed a hand over the man's eyes, closing them. "There was another one down there," he said, still feeling breathless from his own near death experience. "He shot at me. But he's gone now."

Ford looked along the abandoned corridor. "Are you sure?"

"I wasn't hallucinating."

"It's just that he didn't show up on the life signs indicator before," Aiden replied, his eyes remaining suspicious. Carson wasn't ignorant of how the Lieutenant felt about him as a fighter.

"Well maybe he was out of range," Carson shot back. "I didn't imagine seeing him and I certainly didn't imagine being shot at!"

"I— "

"Lieutenant." Teyla's voice interrupted whatever Ford might have said. She gestured toward the wall at Carson's back.

Carson followed the Athosian's gaze. An arc of impact marks shown along the surface mere inches from where his head had been. He gulped.

\--

Kolya's radio beeped and the trio stuttered to a halt. Elizabeth glanced over at the Major. She suspected that his exhaustion wasn't feigned this time. His skin was pale, lines of strain were etched around his mouth and his eyes had taken on a glassy look.

As a voice sounded across the radio link awaiting acknowledgement, they got moving again.

"_Sir, respond." _The voice came again, this time with a heightened edge of alertness to it.

"You're running out of time." A malevolent grin spread across Kolya's face.

"You're just a regular one-track record, aren't you?" John managed in a weak voice. In opposition to the way he sounded and looked, his feet began to move a bit faster, pushing them on toward the brig.

"John . . . ," she started, wanting to tell him to take it more slowly, conserve his strength. But the look he shot her, stopped the comment.

"We're almost to your new home," he said, more for her benefit, she suspected, than Kolya's.

The radio went quiet and stayed quiet.

\--

Rodney was so enthralled with Atlantis' fledging new shield, temporary though it might be that he missed whatever had been said across the Genii radio link. By the time the increased tension in the room registered in his mind, the soldiers had already gone into action. All of them were fiddling with the controls on their radios – changing the frequency, he suspected.

"What's going on?" he demanded, focusing on the nearest guard.

The guard barely spared him a look as he moved into a huddle with the four other soldiers in the control area. They spoke so softly that he was only able to catch a portion of what was being said - something about reinforcements.

"I want to know what's happening," he repeated, more loudly as he closed in on the group. Clearly something was up. Whatever was bad for the Genii had to be good for Atlantis.

A weapon raised in his direction halted his steps. "Something has gone wrong, hasn't it? You might as well tell me what it is. What am I going to do about it anyway? It's pointless to . . . ."

Rodney's words trailed away as the soldier with the raised gun began to move toward him. His expression didn't spawn any thought that he might be rationalized with. He moved into Rodney's personal space and he took a step backward, bumping against the console.

"Or . . . I could stay right here . . . ." Rodney conceded and inched back toward his lap top. "More city saving, stuff." He took the fact that the soldier didn't pulled the trigger as a sign that he could go back to work and set into a furious typing pace on the small keyboard.

The soldier held his position like a hovering shadow half between Rodney and the group of arguing Genii men. It didn't take a scientific genius to figure out that they were arguing about the gate. That one of them pointed emphatically toward the DHD clinched it. But it did take a scientific genius to do what Rodney did next.

\--

"John? Are you all right?"

They'd walked out of the brig in silence, leaving the Genii military leader behind bars. John had moved with single minded determination into the outer corridor and surveyed the surrounding area before half-slumping against the wall and closing his eyes.

"I'm fine. I just need a minute."

Elizabeth nodded, though she was sure he didn't see the action. "I'd imagine something a little longer than a minute is in order."

"A week feels about right." John's eyes creaked open and he shot her a smile. Though tinged with exhaustion, it was good to see.

"So what's next?" she asked. She was over her head in what amounted to a military situation. The next step would be his call.

"Next we see where our back up is." He sorted through the items that he'd stashed in the corridor and pulled out his communicator device and routed it over his ear. "Sheppard to Jumper Two. What's your 20?"

Surprise rolled over his features almost immediately, followed quickly by pride. "They're here on Atlantis," he said between listening to the voice speaking in his ear. The smile faded away from his face as he continued to listen.

"Okay, we'll we're at the brig now. Get here as fast as you can. We'll met you half way." They had taken no more than a few steps when suddenly, without warning, Atlantis was plunged into darkness once again.

**\-- -- **

_Forty-five, forty-four, forty-three. . . . ._ The panicked count down played through Rodney's brain as he half-crawled across the darkened control room, a lap top clutched under one arm. The pounding of his heart all but drowned out the sounds of the confused Genii soldiers, and though he knew intellectually that they shouldn't be able to see him, he expected to feel a bullet slamming into him at any moment.

He crawled past the base of the last console at what his brain identified as second number thirty-one. He was several yards away from the nearest transporter alcove. He had less than thirty seconds to navigate the space, avoiding a couple of support beams, on memory alone. Having programmed Atlantis to shut down for forty-five seconds before opening the transporter door and locking out all gate functions.

A bright beam cut through the darkness, making an arc somewhere above his head. He froze, nearly losing the lap top in the process. Several tense panicky moments passed before he realized that he'd forgotten to count.

"He's gone!" A voice yelled. Probably the guard who'd had the gun on him, Rodney decided. Torn between keeping absolutely still and making a run for it, his mind latched onto a compromise. The quick flashing of light had revealed his proximity to one of the support beams.

_Not cut out for this, not cut out for this, not cut out for this_ played through his mind as he struggled not to breathe so loud and made for the column. Where were the military types when you needed them? Ducking downward as low as he could, he concentrated on sounds the men were making. Other lights began to flash around the room behind him.

Cursing himself for losing track of time, he began to crawl straight out toward what he hoped was the transporter alcove. The lights could come back up at any moment, and he wanted to be close enough to dive into the parting doors. He kept crawling until his head bumped against something sending off sparks behind his eyes. The lap top clattered to the floor echoing in the room like a shot.

The lights came back up.

"There he is!"

Rodney reacted. Shots rang out behind him as he ran the few steps into the open transporter alcove. He thought he felt a bullet fly past before he crashed against the inner wall and down onto his backside. The doors began to slide shut just as one of the running soldiers stopped and took aim.


	9. Part 9

**Notes for the Chapter:**

> **Part Nine**

**Part Nine**

"You've got to be kidding me!" John declared to the darkness. "Enough already!" Trying to remain positive was becoming a challenge in the current situation.

"Perhaps it's an effect of the storm," Elizabeth's voice reached him in the darkness, offering a possible explanation.

"Yeah. Maybe," he agreed, fingering the switch on his P90 that turned on the built in light. "All a part of McKay's plan?"

An expressively raised brow revealed that she wasn't discounting the idea.

Realizing she was right, he stifled a chuckle and keyed on his radio.

"Ford?"

"Here, Sir," came the reply. "When the lights went down the prisoners attempted to escape, but we took care of the situation." Sheppard couldn't resist the half grin at the tone in Ford's voice as he made his report. He couldn't imagine that Sora wouldn't appreciate her present predicament.

"We're still moving in your direction," Ford continued with his report. "It would be a lot easier though if the lights stayed on."

"Can't argue with that," John agreed. "How far out are you?"

"Ten minutes. Maybe less. Kinda hard to tell in the dark." Ford had barely completed the statement when Atlantis re-illuminated.

"The power of positive thinking . . . ." John said, looking about, half anticipating that the lights would go down again.

"I think we're picking you up on the life signs detector," Ford's said. "Wait. . . Sir!" His voice was suddenly filled with alarm. "I'm registering a third life sign!"

John cursed and spun, leveling his P90 on the corridor behind them. Every nerve ending seemed to protest the movement. Thankfully the area was clear.

"Where, Ford?" He demanded into the radio. "How close?" One handedly he reached into his flak jacket and removed his own detector and handed it to Elizabeth. His attention remained on scanning the area, alert for any hint of movement.

"They've moved out of range, Sir," Aiden said. "I can't see them anymore."

"We're going to have to work on figuring out how to get that range extended," he muttered, then shot a glance toward Elizabeth to see what their device told them. The frown on her face brought an even deeper frown to his.

"What's wrong?" he asked, moving in closer. Even from a distance the screen seemed dimmer than usual.

"Is this the way it should work?" Elizabeth asked, handling the item to him.

Shooting a glance outward, still alert, though he knew Ford would cue him if he saw anything close, he took the detector. The blips that shown – far too many to represent reality – were fading in and out. Never a good sign with technology.

He sighed. "It must have gotten damaged when Kolya and I were fighting." Something else for McKay to fix when they got out of this.

\--

The doors closed just as the sounds of the bullets impacted against the outer surface. Too frightened to even more or breathe, Rodney remained frozen in his position on the floor as he dematerialized and was transported elsewhere on Atlantis.

When the transport was complete, he still remained seated on the floor for several long moments waiting for his heart to start beating again. Then, slowly, he opened the lap top, hoping that the industrial level UL certification meant that the device would survive being drop tested at least once more.

The screen came to life like a loyal pet. He half smiled at that positive bit of news. He immediately linked into the now pass worded system and deactivated the transporter alcoves. Next, he went in search of the frequency of the radios that the team used.

\--

** _This is McKay, calling anyone on the mainland or nearby. Please respond. _ **

The voice boomed across the radio link reverberating through Sheppard's head. Happy to hear the voice, aggravated at the volume and bemused that the voice had sounded just as he'd thought of his repairing the broken life signs scanner. "McKay? That you?"

He met Elizabeth's equally surprised gaze as he awaited the response.

"Of course, it's me. Didn't I identify myself?" came the returned response. That was his McKay all right. A grin spread across his face as Ford, Teyla and Beckett all announced their presences over the radio link.

"What happened? Where are you?" John cut across the chatter. "Last time I saw you, you were stuck in command with the bad guys."

"I managed a little plan to get away. Which I see you've done as well." Rodney replied smugly. "Shall I assume since the gang's all here that we have a plan?"

"Uh. . . we're working on that," John told him. "But first, where are you? And please tell me that you didn't leave the Genii all alone in the gate room."

"Well first of all, I'm in a transporter alcove," Rodney replied, his back clearly up. "And second of all, yes I did."

"You what?!" John demanded. "What's stopping them from bringing more through the gate? It's bad enough that we still have to get rid of the ones that are already here. What were you thinking?"

"Are you done?" Rodney asked.

"Not hardly. But I'll feel better if you tell me there was a good reason for what you did."

"Of course there was. They don't just hand out degrees in physics to complete morons. In fact, considering the things I've accomplished today alone . . . ."

"McKay. . . ." John started warningly.

"Right. I, in spite of your obviously low opinion of my reasoning ability, locked out the control room and routed it through my lap top. We'd already begun the process when we set up the capturing protocol. It was just a simple matter of a small pass coded routine to take over from there. No one's coming or going through the gate or doing anything else in the control room unless they have either my pass code or the ATA gene."

"Ah," Sheppard nodded, impressed. "So that last power outage . . . that was you?"

"It was." The smug smile was evident in his voice.

"What else can you do?"

"I can locate all of the life signs in the city."

John felt a plan forming. "Do it."

* * *

A/N: I'll admit it. I was weak. I started watching "The Eye", after I'd written this chapter, thinking that I was far enough along that I could indulge myself without fear of mixing the two. Well, when I got to a certain section when John did something that McKay would do I was astounded at a similarity between the episode and my story. So, I hit the stop button and turned off the ep. And it was sooo exciting, too! And now I'm really on pins and needles to finish this thing. Plus – January's coming!

There is another chapter complete after this one, which I will post tomorrow. After that, one more chapter to go! Hope everyone is still enjoying the story.


	10. Part 10

**Notes for the Chapter:**

> **Part Ten**

**Part Ten**

"Dr. Weir! Major Sheppard!" Carson couldn't hold back the exclamation at seeing his city-mates. Acting as guard and escort to prisoners wasn't really his strong suit. And holding the gun on them, with the intention of possibly pulling the trigger, just felt wrong.

Elizabeth greeted them all with a bit of a smile and a nod of her head.

John's greeting was much more hurried as he took command of the situation. "Let's get our guests to detention," he ordered, then turned to lead the way.

Carson frowned as the major moved. In the dim corridor lighting, he caught what he suspected was the remnants of blood on the major's temple. The pale complexion and the exhausted demeanor were a little harder to miss. Then there was the stiff way he moved, and even, he realized, a slight limp!

"Hold on, Major! Not so fast!" He moved around the rest of the group to catch up to the lead man. Sheppard's back stiffened slightly, but he did stop.

Carson moved around to face him, and took in his expression. "Hoping I wasn't going to notice, were you?"

"Maybe," John admitted, "But either way it doesn't matter. We don't have time for this. We've got . . . ."

Carson tuned out the words as he caught sight of the cloth darkened with blood which was tied around one of the major's thighs. And then there was the dry blood on one raggedly torn sleeve. Truly, the things humans did to one another were truly appalling.

With a sigh and a shake of his head, he reached into his pocket and withdrew a small flash light. "Just one little examination," he said in his best conciliatory tone. He shone it into the major's eyes.

"Didn't you hear me?" John winced at the light and swatted at his hand. "We don't have time for this!"

"Yeah, I did hear you," Carson lied. "But this should only take a moment more." He hadn't exactly needed to listen to the words to know what he'd said. This was Major Sheppard, after all. And there were bad guys out on the lam. Even injured, the man would only stay down if he was unconscious.

"Your pupils look okay." He dropped the flash light into his pocket and tried for a careful look at the arm wound. "You've lost a bit of blood and are suffering from exhaustion. I've a suspicion that there's further damage that you're not letting on about. It's my educated opinion that you need to be in the infirmary having those wounds looked after."

"As long as there are invaders in the city, we don't have an infirmary, doc. No place is safe and we're just wasting time here. As soon as the city is clear, I'll surrender myself to you."

Carson knew that was the best offer he was likely to get, but still he felt inclined to argue. A touch on his arm drew his attention to Elizabeth.

"I don't like it any more than you do, but he's right, Carson."

"Aye." He acquiesced then fell in line as they led the rest of the prisoners to the brig.

\--

Accessing all of the systems wasn't as easy on the lap top as it was in the control room. It took longer to work his way through all of the screens and sub-menus. Finally he found the city's life signs detecting function.

Lifting the lap top a little he spoke into the small microphone. "McKay here. I'm in the system now."

"Good." Sheppard's voice came back through the computer's speakers. "Where are they?"

Rodney tapped a few keys to get the view he needed. "First I need a baseline. How many are in your area?"

"Eight, plus one in the brig."

"Right." McKay went to work. The blips displayed beautifully on the screen. "I've got your eight, but . . . . nothing in the brig, and . . . ." he hit a control key and switched to another view. "Everyone else is either in the control room or seems to be moving toward it."

"Did you say _nothing_ in the brig?" Sheppard demanded.

Rodney rolled his eyes. Why was he having to repeat himself? He double checked the monitor anyway, though. "Like I said, nothing in the brig."

"Are you sure?"

"Of course, I'm sure," Rodney snapped. "Who is supposed to be there, anyway? Perhaps they've committed . . . ." His voice trailed away as he realized who was most likely locked away and what had no doubt happened. "Oh no. . . ."

"Oh no? What oh no? There's no oh no! What did you do McKay?" The major's voice came across labored as if they were moving more quickly. The blips showing on the screen revealed that to be the case. And they were closing in fast on the now empty brig.

Rodney gulped then began to explain. "The command I used after the shut down was an open doors command. It may have caused the brig doors to release."

"What?!" Sheppard had worked himself up into a righteous fury. "What did you do that for?! What if there were prisoners there?!"

Guilt washed over Rodney, but still he fought. This wasn't entirely his fault, after all. Not really. "I didn't exactly have time to refine the door code," he said, feeling more justified in his actions. "I was trying to prevent our not-so-invited guests from bringing more friends and family. Besides, how was I supposed to know there was anyone there? I'm not psychic! I had no way of knowing that you were running around playing hero and that I was ruining your game!"

Sheppard was quiet for a few moments and Rodney wondered if he'd gone too far. But then John spoke, his voice calmer. "Well, we're working together now. We're leaving three prisoners in the brig. Can we make sure they stay here?"

"Do-able," McKay responded in an equally subdued voice.

"Good. Now we need a plan."

\--

John pressed on, trying to keep up a good front for the other four people who were with him. This thing had to end soon because he wasn't sure he had much left. In the relative calm of making their way back toward the control room, via a small detour to the weapons locker, there wasn't much of an adrenaline boost to keep him going. And he worried that if he stopped that would be all she wrote. But with the odds running just over two Genii to each Atlantean, they'd need every advantage that they could get.

"They're moving." Rodney's voice sounded in his ear.

"What? Where?" John asked, suddenly more alert.

"It looks like it's towards . . . . the jumper bay." Rodney's voice rose. John felt the same dread trickling through his system.

"Will they be able to activate the gate with the jumpers?"

Rodney hesitated. "Yes. If they can activate them."

John cursed. "See what you can do to stop that!" He turned toward the rest of them. "Time for plan B."

* * *

A/N: Okay, folks. One more chapter.


	11. Part 11

**Notes for the Chapter:**

> Author's Note: The final chapter. Thank you for all of the wonderfully encouraging reviews. There were times when writing this felt a little daunting, but it is complete at last! I hope you've all enjoyed it!

Author's Note: The final chapter. Thank you for all of the wonderfully encouraging reviews. There were times when writing this felt a little daunting, but it is complete at last! I hope you've all enjoyed it!

**Part Eleven**

John eyed his new, functioning, life-signs detector as he crept along the dim corridor. The low, intermittent drone of a voice reached his ears as he drew closer to the lower level entry into the gate room.

"McKay?" he called softly into the radio link. "How're we looking?"

"There are still two in the gate room and two in the control room. Jumper bay has six. Looks like they've found jumper one. Everyone is moving toward it."

"What is different about jumper one?" Teyla sounded in the middle of conversation.

"Anyone can use it." Sheppard replied, hoping to prevent either scientist from going into a long-winded explanation about genes and mental commands. "Which is why we need to move. Everyone. By the numbers."

John moved the remaining yards toward the gate room, stopping short near the doorway. The life-signs detector shown that one of the guards stood just a couple of yards away on the opposite side of the wall.

He slipped the clear mask down over his head, then tapped three times against the open radio link. Four answering taps sounded back, indicating that Elizabeth had likewise put on her mask and was in place outside of the other doorway which led into the gate room from the opposite side.

Five more taps came from Ford and Teyla's teams announcing that they had taken up their positions near the jumper bay and were ready to move. All that remained was for McKay to call the go-ahead so that they could begin the simultaneous attack that had become their plan B.

"Oh crap! They're starting to activate the gate. Go! Go! Go! Go Now!"

John reacted. The canister that he'd retrieved from the weapons locker was quickly activated and tossed around the door into the room. A startled cry reached his ears followed by the ensuing chaos from the jumper bay and the reaction of the two men in the control room.

Amid the noice, he called "Now!" across the link, bent low and entered the gate room.

Across the distance, he saw Elizabeth's masked form doing the same thing. Ignoring the incongruity of seeing her decked out in military gear, wearing a face mask and carrying a P90, he made for his target. The cursing, coughing, half-blinded soldier was making a valiant effort to reach for his weapon. It fell from his fingers to the floor.

John reached him in time to kick it away toward the center of the room before he caught a movement from above. He fired instinctively before ducking behind the curving stairs. More shots sounded before he risked taking a couple of more shots from around the staircase.

The downed Genii soldier jerked and whimpered as he was hit by friendly fire. But it was the cry that he caught in his ear piece that frightened him. Elizabeth.

Before John could speak, Rodney's frantic cries burst over the radio link, demanding to know if she was all right. John could barely get a word in edgewise, and the last thing he needed was panic rippling throughout the team.

But, Elizabeth's voice sounded back over the link. "I'm fine," she said, her voice only slightly shaky. "I wasn't hit."

John wasn't sure he bought that, and sought to form his own opinion. He ducked back out from behind his cover and fired upward. One of the shots found its mark and a body dropped to the floor from above.

Risking a peek out around the steps he caught sight of Elizabeth. She was trying to get to one of the still moving Genii so that she could put the temporary restraints on him. She was favoring her right hand, holding it in close to her body. The weapon she'd been carrying lay several yards away on the floor. They made eye contact across the expanse.

"I'm fine, John." She mouthed the words.

There were a lot of things that he wanted to say to that, but didn't have the luxury of time or place. He satisfied himself with a mouthed 'later' before turning his attention back to the problem at hand.

"Ford? How're you doing up there?" he spoke across the link.

"Rounding them all up, Sir," was the response.

"Good. Teyla, get to the gate room, help Dr. Weir."

Before Teyla's returned response sounded, another voiced sounded in the room. This one loud and daring.

"Major Sheppard! Do not think that you have won."

Kolya.

John leaned back into wall, thinking. Already the specialized tear gas was dissipating, what remained would not be strong enough to have much of an effect on the Genii leader. He needed to get in closer to do any real damage.

"I've captured all of your men," he called. "This is what we like to call, 'Checkmate'. Or, in simple terms, 'you lose'! So why don't you just surrender and save me the trouble of coming after you?"

"Another weakness of yours, Major. We Genii don't make things easy."

"Yeah, I didn't think you would," John murmured and withdrew the last remaining canister of tear gas. He gauged its weight against the distance to the spot that Kolya's voice had come from.

"More about us being the weakest link?" John called. Then, ignoring the objection of bruised ribs, he drew back and threw with all of his might before quickly ducking back around the steps. Several shots sounded, but amid them he heard the satisfying sound of the canister landing against the balcony floor. He did a slow Mississippi count to three and looked again.

The great Genii military leader was retreating away from the spraying container, covering his mouth with a piece of cloth. Taking advantage of the moment, John moved, taking the stairs two at a time in an attempt to reach the top in one piece.

Kolya remained ahead of him, seeking a means of escape from the pervasive chemicals. He disappeared through the doors into the driving rain of the storm outside. John followed, his mind tripping over the small item that was tossed back through the sliding door. John wasn't sure what it was, but he figured it wasn't good.

He reached for the device, catching it in mid-air, losing his P-90 in the process. There was no time to think about consequences or potential outcomes, all he could do was run. He cleared the sliding glass door and sighted Kolya moving farther along the balcony, obviously seeking cover.

"Here! Catch!" John called as he let the object fly directly toward the other man.

Kolya's eyes widened as the object sailed toward him. He raised his arms in an attempt at self protection, but in the end it did him no good. The device exploded.

The small concussive force knocked John off balance, sending him landing hard on his backside. It was a jarring experience, and all he wanted to do was just lay back, regardless of the chilly-ness of the rain, and let the world fade from existence. But there was one more thing he had to do.

Struggling up onto hands and knees he got his legs back under him, tossed the mask aside, then made his way over to Kolya. He had to be sure. The Genii's eyes were open in death, not reacting to the rain that splattered against him, washing away the flecks of red that dotted his neck.

"Turns out you were the weakest link, after all." He turned away, surprised when his legs threatened to give out. The irony of his final words to Kolya and the reality of his own weakened condition brought a grin to his lips. He would have chuckled, but that would have hurt far too much.

He managed the remaining steps that got him through the sliding doors back inside out of the weather. He heard the familiar sound of running footsteps and looked up to see Teyla and Weir headed toward him, both still wearing masks.

He let his back rest against the wall, hoping distantly that the gases had cleared out. His perspective shifted and it was a moment before he realized that he was sliding slowly downward. One of the women said something, but his brain didn't even try to understand. It faded into the haziness of the moment and the room seemed to brightened before fading to white.

\--

John opened his eyes. For several long moments he felt as if he was floating, everything was hazy and had an unreal feel to it. Then, gradually, the fuzziness coalesced into a familiar room. The infirmary.

Not exactly his favorite place, but he couldn't seem to work up the energy to even consider moving, much less getting out of bed. That didn't stop the slight tickling in the back of his mind that told him that he was missing something. Then, suddenly, it came back to him. It was the sound and feel of every day business in the city. Soft footsteps moved somewhere in another part of the infirmary; muted voices making the sounds of normal conversation, all was right with the world.

He felt the urge to smile, but closed his eyes instead. The lazy, cotton-lined world returned, and then there was nothing.

When John next opened his eyes it was much more quickly and in reaction to something that was just on the edge of his perception. He looked around, a frown between his brows as he tried to figure out where he was and what was going on.

"Is he in here?" a disembodied voice demanded. McKay's voice.

He remembered then, and struggled toward a more upright position. Mistake. Whatever meds Beckett had been feeding him weren't up to the task of dealing with sudden movements. Every aching portion of his body chose that moment to chime in as well. There wasn't much hope of stifling his grunt of pain – and just when both Dr. Beckett and McKay showed up around the privacy curtain.

"Now look what you've done," Beckett exclaimed, shooting a look toward the astrophysicist before moving to John's side and starting in on the doctor thing. "He needs more rest."

"I'm fine," John objected, disappointed with the dry, tired sound of his voice. "Just moved too fast is all."

"That's your body's way of telling you to be more careful in the future. You took quite a beating, ya know. And whatever Dr. McKay needs can surely wait until a little later."

"I just came to make sure you weren't milking this injury thing for all it's worth. There is a lot of work to be done around here, you know."

"Me?" John barely choked back a laugh. Another mistake his body warned him about. "I'm hardly that person. But if you're here to thank me for saving the day, I'm all ears."

"Surely, you jest," Rodney responded. "I believe I'm the one who thought of the alternate plan to save the city. While you were sleeping it off here in the infirmary, it was my plan that brought the shield online long enough to weather the worst of the storm. It was –."

"Are we interrupting?" Another voice sounded as Dr. Weir, Teyla and Ford appeared around the curtain as well. He didn't miss the white bandaging on her hand.

"As a matter of fact . . . ."

"No." John cut in, ignoring Rodney's aggravated look.

"Good to see things are back to normal," Weir replied with a satisfied smile. Then, "How are you feeling?"

John caught himself before he shrugged and smiled instead. "Fine. How's the hand?"

She looked down at the appendage. "Carson tells me that I'll be back to gun toting in no time."

That caught John by surprise, and he couldn't hold back a laugh. He paid for it. Weir looked apologetic.

"You were pretty proficient out there," he told her. "Was that part of your diplomatic training?"

Elizabeth completely ignored the question. "I did what I could to help. I think all of you worked well together and had a part in saving this city. Commendations will be added to all of your records."

"We did make one heck of a team didn't we?" Beckett spoke up.

"We did," Rodney smiled smugly.

"Now that everyone is safe and happy," John spoke up, "What does a guy have to do to get some food around here?"

The End


End file.
